总是报错：'str' object is not callable in my snakemake for RNA-seq workflow

Question

我想用 snakemake 编写我的 RNA-seq 管道，但它总是报告相同的 errors.It 让我很烦！

下图显示当前文件夹下的整个文件。

|-- 01_raw
|   |-- epcr1_1.fastq
|   |-- epcr1_2.fastq
|   |-- epcr2_1.fastq
|   |-- epcr2_2.fastq
|   |-- wt1_1.fastq
|   |-- wt1_2.fastq
|   |-- wt2_1.fastq
|   `-- wt2_2.fastq
|-- 02_clean
|   `-- id.txt
|-- Snakefile
`-- Snakemake2.py

Snakefile里有我的全部内容

SBT=["wt1","wt2","epcr1","epcr2"]


rule all:
    input:
        expand("02_clean/{nico}_1.paired.fq.gz","02_clean/{nico}_2.paired.fq.gz",nico=SBT)

rule trim_galore:
    input:
        "01_raw/{nico}_1.fastq",
        "01_raw/{nico}_2.fastq"
    output:
        "02_clean/{nico}_1.paired.fq.gz",
        "02_clean/{nico}_1.unpaired.fq.gz",
        "02_clean/{nico}_2.paired.fq.gz",
        "02_clean/{nico}_2.unpaired.fq.gz",
    log:
        "02_clean/{nico}_qc.log"
    shell:
        "Trimmomatic PE -threads 16 {input[0]} {input[1]} {output[0]} {output[1]} {output[2]} {output[3]} ILLUMINACLIP:/software/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 &"

当我用命令"snakemake -np"给它dry_run的时候，希望它能运行顺利，但是总是报同样的错误：

TypeError in line 6 of /root/s/r/snakemake/my_rnaseq_data/Snakefile:
'str' object is not callable
  File "/root/s/r/snakemake/my_rnaseq_data/Snakefile", line 6, in <module>

第 6 行是

expand("02_clean/{nico}_1.paired.fq.gz","02_clean/{nico}_2.paired.fq.gz",nico=SBT)

不知道怎么回事。让我烦了一整天！希望有人能帮忙me.Thanks提前！

Answer 1

问题在于您在 rule all 中使用 expand 函数的方式。 expand 作用于一根弦，但您提供了两根。这会起作用：

rule all:
    input:
        expand("02_clean/{nico}_1.paired.fq.gz", nico=SBT),
        expand("02_clean/{nico}_2.paired.fq.gz", nico=SBT)

或者，您可以进一步简化：

rule all:
    input:
        expand("02_clean/{nico}_{n}.paired.fq.gz", nico=SBT, n=[1,2])

总是报错：'str' object is not callable in my snakemake for RNA-seq workflow

always report errors: 'str' object is not callable in my snakemake for RNA-seq workflow

snakemake

rna-seq